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A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

ABSTRACT: BACKGROUND:Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. RESULTS:A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within 'Hongyang' The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned 'Hort16A' cDNAs and comparing with the predicted protein models for Red5 and both the original 'Hongyang' assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised 'Hongyang' annotation, respectively, compared with 90.9% to the Red5 models. CONCLUSIONS:Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis.

SUBMITTER: Pilkington SM

PROVIDER: S-EPMC5902842 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

Pilkington Sarah M SM Crowhurst Ross R Hilario Elena E Nardozza Simona S Fraser Lena L Peng Yongyan Y Gunaseelan Kularajathevan K Simpson Robert R Tahir Jibran J Deroles Simon C SC Templeton Kerry K Luo Zhiwei Z Davy Marcus M Cheng Canhong C McNeilage Mark M Scaglione Davide D Liu Yifei Y Zhang Qiong Q Datson Paul P De Silva Nihal N Gardiner Susan E SE Bassett Heather H Chagné David D McCallum John J Dzierzon Helge H Deng Cecilia C Wang Yen-Yi YY Barron Lorna L Manako Kelvina K Bowen Judith J Foster Toshi M TM Erridge Zoe A ZA Tiffin Heather H Waite Chethi N CN Davies Kevin M KM Grierson Ella P EP Laing William A WA Kirk Rebecca R Chen Xiuyin X Wood Marion M Montefiori Mirco M Brummell David A DA Schwinn Kathy E KE Catanach Andrew A Fullerton Christina C Li Dawei D Meiyalaghan Sathiyamoorthy S Nieuwenhuizen Niels N Read Nicola N Prakash Roneel R Hunter Don D Zhang Huaibi H McKenzie Marian M Knäbel Mareike M Harris Alastair A Allan Andrew C AC Gleave Andrew A Chen Angela A Janssen Bart J BJ Plunkett Blue B Ampomah-Dwamena Charles C Voogd Charlotte C Leif Davin D Lafferty Declan D Souleyre Edwige J F EJF Varkonyi-Gasic Erika E Gambi Francesco F Hanley Jenny J Yao Jia-Long JL Cheung Joey J David Karine M KM Warren Ben B Marsh Ken K Snowden Kimberley C KC Lin-Wang Kui K Brian Lara L Martinez-Sanchez Marcela M Wang Mindy M Ileperuma Nadeesha N Macnee Nikolai N Campin Robert R McAtee Peter P Drummond Revel S M RSM Espley Richard V RV Ireland Hilary S HS Wu Rongmei R Atkinson Ross G RG Karunairetnam Sakuntala S Bulley Sean S Chunkath Shayhan S Hanley Zac Z Storey Roy R Thrimawithana Amali H AH Thomson Susan S David Charles C Testolin Raffaele R Huang Hongwen H Hellens Roger P RP Schaffer Robert J RJ

BMC genomics 20180416 1

<h4>Background</h4>Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models.<h4>Results</h4>A second genome of an A. c ...[more]

PMID: 29661190

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Project description:Pseudomonas syringae pv. actinidiae (Psa) is a bacterial pathogen of kiwifruit. This pathogen causes leaf-spotting, cane dieback, wilting, cankers (lesions), and in severe cases, plant death. Families of diploid A. chinensis seedlings grown in the field show a range of susceptibilities to the disease with up to 100% of seedlings in some families succumbing to Psa. But the effect of selection for field resistance to Psa on the alleles that remain in surviving seedlings has not been assessed. The objective of this work was to analyse, the effect of plant removal from Psa on the allele frequency of an incomplete-factorial-cross population. This population was founded using a range of genotypically distinct diploid A. chinensis var. chinensis parents to make 28 F1 families. However, because of the diversity of these families, low numbers of surviving individuals, and a lack of samples from dead individuals, standard QTL mapping approaches were unlikely to yield good results. Instead, a modified bulk segregant analysis (BSA) overcame these drawbacks while reducing the costs of sampling and sample processing, and the complexity of data analysis. Because the method was modified, part one of this work was used to determine the signal strength required for a QTL to be detected with BSA. Once QTL detection accuracy was known, part two of this work analysed the 28 families from the incomplete-factorial-cross population that had multiple individuals removed due to Psa infection. Each family was assigned to one of eight bulks based on a single parent that contributed to the families. DNA was extracted in bulk by grinding sampled leaf discs together before DNA extraction. Each sample bulk was compared against a bulk made up of WGS data from the parents contributing to the sample bulk. The deviation in allele frequency from the expected allele frequency within surviving populations using the modified BSA method was able to identify 11 QTLs for Psa that were present in at least two analyses. The identification of these Psa resistance QTL will enable marker development to selectively breed for resistance to Psa in future kiwifruit breeding programs.

Dataset Information

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

Publications

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

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